dps:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|dps}}{{Tab On|Gene|dps}}{{Tab|Gene Product(s)|dps}}{{Tab|Expression|dps}}{{Tab|Evolution|dps}}{{Tab|On One Page|dps}}{{TabsBottom}}
{{Tab|Quickview|dps}}{{Tab On|Gene|dps}}{{Tab|Gene Product(s)|dps}}{{Tab|Expression|dps}}{{Tab|Evolution|dps}}{{Tab|On One Page|dps}}{{TabsBottom}}
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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|  id="G46a9b93ee795b"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''dps''  
''dps''
|-
!align=left {{table_heading_style}} |Mnemonic
||
DNA-binding Protein from Starved cells
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0801, b0812, JW0797, pexB, vtm''<ref name='LIB:Riley_2006'/>, vtm''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12179.G46a9b93ee795b&page=12179&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0801, b0812, JW0797, pexB, vtm''<ref name='LIB:Riley_2006'/>
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{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b93f6c062"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
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MG1655
MG1655
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18.27 minutes&nbsp;
18.27 minutes&nbsp;
|
|
MG1655: 848134..847631<br />{{GBrowseFigureByCoord|846631|849134|ecoli|MG1655}}
MG1655: 848134..847631<br /><gbrowseImage>
name=NC_000913:847631..848134
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11415 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11415 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:846631..849134 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|846631|849134|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:847631..848134&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|847631|848134|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11415 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11415 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 841536..841033<br /><gbrowseImage>
name=NC_012967:841033..841536
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|841033|841536|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|841033|841536|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 750599..751102<br /><gbrowseImage>
name=NC_012759:750599..751102
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|750599|751102|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|750599|751102|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 849333..848830<br />{{GBrowseFigureByCoord|847830|850333|ecoli_W3110|W3110}}
W3110: 849333..848830<br /><gbrowseImage>
name=NC_007779:848830..849333
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:847830..850333 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|847830|850333|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:848830..849333&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|848830|849333|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 902062..901559<br /><gbrowseImage>
name=NC_010473:901559..902062
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|900553|903068|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|900553|903068|FASTA Dump}}
 
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<!--Location_notes--></protect>
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9b940157fc"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
847634
|
Edman degradation
|
PMID:7984106<br />PMID:8354462<br />PMID:9298646<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b94055a66"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-
|
&Delta;dps (Keio:JW0797)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107125 CGSC8844]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0002776 dps::Tn5KAN-2] (FB20241)
|
Insertion at nt 212 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20241]
|
does not contain [[pKD46]]
|-
|
''&#916;dps-784::kan''
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
PMID:16738554
|
|
&nbsp;
[[cgscmutation:100646|CGSC:100646]]
|
|
&nbsp;
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D4e04ba1353f68"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9b940f2db5"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0797
JW0797
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTCGATGTTAGACTCGATAAA  
Primer 2:CCTTCGATGTTAGACTCGATAAA  
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[[:Category:Kohara_Phage:10A8|10A8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=205 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4C6|4C6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=206 Genobase]
|
PMID:3038334
|-
|
zbh-29::Tn10
|
Linked marker
|
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 37% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10
|-
|
zca-1230::Tn10
|
Linked marker
|
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbj-1230::Tn10
 
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{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b94187954"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11415 EcoCyc:EG11415] 
EcoCyc:EG11415
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1387 EchoBASE:EB1387] 
EcoGene:EG11415
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0812 EcoliGenExpDB:b0812] 
RegulonDB:ECK120001381
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0898 ECOL199310CYC:C0898]
[http://www.ncbi.nlm.nih.gov/gene?term=945101 GeneID:945101]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11415 EcoGene:EG11415] 
EchoBASE:EB1387
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=DPS ECOO157CYC:DPS] 
ASAP:ABE-0002776
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12179.V46a9b94187954&page=12179&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/31650 CGSC:31650] 
|
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===Notes===
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==Links==
==Links==
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__NOTOC__
__NOTOC__
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:dps genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 19 September 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

dps

Mnemonic

DNA-binding Protein from Starved cells

Synonyms

ECK0801, b0812, JW0797, pexB, vtm[1], vtm

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

18.27 minutes 

MG1655: 848134..847631
<gbrowseImage> name=NC_000913:847631..848134 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 841536..841033
<gbrowseImage> name=NC_012967:841033..841536 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 750599..751102
<gbrowseImage> name=NC_012759:750599..751102 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 849333..848830
<gbrowseImage> name=NC_007779:848830..849333 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 902062..901559
<gbrowseImage> name=NC_010473:901559..902062 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

847634

Edman degradation

PMID:7984106[2]
PMID:8354462[3]
PMID:9298646[4]


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

Δdps (Keio:JW0797)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC8844[6]

dps::Tn5KAN-2 (FB20241)

Insertion at nt 212 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB20241

does not contain pKD46

Δdps-784::kan

PMID:16738554[5]

CGSC:100646


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0797

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAGTACCGCTAAATTAGTTAA

Primer 2:CCTTCGATGTTAGACTCGATAAA

10A8

Kohara Phage

Genobase

PMID:3038334[9]

4C6

Kohara Phage

Genobase

PMID:3038334[9]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[6]

est. P1 cotransduction: 37% [10]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[6]

est. P1 cotransduction: % [10]
Synonyms:zbj-1230::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11415

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11415

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001381

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945101

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1387

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002776

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Altuvia, S et al. (1994) The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol. Microbiol. 13 265-72 PubMed
  3. ↑ Foster, SJ (1993) Purification and characterization of an 'actomyosin' complex from Escherichia coli W3110. FEMS Microbiol. Lett. 110 295-8 PubMed
  4. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  5. ↑ 5.0 5.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  8. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  9. ↑ 9.0 9.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  10. ↑ 10.0 10.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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